Wastewater irrigation will result in nitrogen pollution in groundwater systems. But sometimes fresh water irrigation may produce more serious problems in N pollution. To discuss the influence of geochemical conditions and irrigation ways to N pollution, tests on 8 soil columns with 9.6 cm internal diameter and 200 or 130 cm height for more than one year and a one year monitoring investigation in situ were carried out. It was found that a combined effect of nitrification and denitrification existed in the environment of paddy fields. The combination was influenced strongly by the depth of groundwater table. If the depth was less than 100 cm, the process of nitrification and denitrification would make less contribution to the removal of nitrogen. If it is more than 170 cm, the process would be remarkable; Nitrification developed adequately in the environment of dry farmland, but denitrification developed only to a certain degree. In spite of this, dinitrification still played an important role in the protection of groundwater against N pollution, combined with the effects of dilution and volatilization: in the groundwater systems recharged by wastewater irrigation, hydrogeological structures and irrigation ways were the major factors controlling nitrogen transportation and pollution. With this base, six models were divided among which nitrogen pollution was minimum in model 6 and maximum in model 1 and model 3.